2.1 Primary Analysis - Sequence processing
- - BIER's pipeline
  - CNAG's pipeline

2.1 Primary Analysis - Sequence processing

After sequencing, reads are mapped to the human genome reference (GRCh37). Then, there are some filtering steps in which the number of reads decreases until variant calling. Here, we describe how this reduction occurs in each pipeline.

BIER's pipeline

In this pipeline, there are four stages where the number of reads decreases (mapping, filter by mapping quality, remove duplicates and intervals realignment). This table shows reads remaining after these stages.

N_reads_forward and reverse: initial number of reads forward and reverse obtained in the exome sequencing process
N_mapped_read_pairs: number of read pairs mapped to the human genome reference
%_mapped_read_pairs: percentage of initial read pairs mapped to the human genome reference
N_mapped_reads_mapq>10: number of mapped reads whose mapping quality (mapq) is higher than 10
%_mapped_reads_mapq>10: percentage of initial mapped reads whose mapping quality (mapq) is higher than 10
N_reads_single_hit: number of reads uniquely mapped to the human genome reference without duplicates
%_reads_single_hit: percentage of initial reads uniquely mapped to the human genome reference without duplicates
N_reads_single_hit_realigned: number of reads located in the exome capture kit targets who had been realigned
%_reads_single_hit_realigned: percentage of initial reads located in the exome capture kit targets who had been realigned

Sample	N_reads forward	N_reads reverse	N_mapped read_pairs	%_mapped read_pairs	N_mapped reads mapq>10	%_mapped reads mapq>10	N_reads single_hit	%_reads single_hit	N_reads single_hit realigned	%_reads single_hit realigned
SGT038	31471997	31471997	31304563	99.47	32844926	52.18	28115216	44.67	22724178	36.10
SGT077	27308034	27308034	27166800	99.48	28443473	52.08	24680760	45.19	20024427	36.66
SGT161	27566691	27566691	27429566	99.50	28775620	52.19	24997317	45.34	20213242	36.66
SGT187	29730857	29730857	29593092	99.54	31001122	52.14	26579044	44.70	21530503	36.21
SGT230	30415770	30415770	30296046	99.61	31712462	52.13	27084895	44.52	22377265	36.79
SGT238	29472514	29472514	29333890	99.53	30770469	52.20	26406037	44.80	21543680	36.55
SGT241	29513223	29513223	29365739	99.50	30803708	52.19	26174909	44.34	21579194	36.56
SGT274	30394832	30394832	30268625	99.58	31699515	52.15	27122226	44.62	22387721	36.83

CNAG's pipeline

In contrast with BIER's pipeline, there are only two stages where the number of reads decreases (mapping and remove duplicates).

N_reads_forward and reverse: initial number of reads forward and reverse obtained in the exome sequencing process
N_mapped_read_pairs: number of read pairs mapped to the human genome reference
%_mapped_read_pairs: percentage of initial read pairs mapped to the human genome reference
N_read_pairs_single_hit: number of read pairs uniquely mapped to the human genome reference remaining after removing duplicates
%_read_pairs_single_hit: percentage of initial read pairs uniquely mapped to the human genome reference remaining after removing duplicates

Sample	N_reads_forward	N_reads_reverse	N_mapped read_pairs	%_mapped read_pairs	N_read_pairs single_hit	%_reads_pairs single_hit
SGT038	31471997	31471997	27098380	86.10	26533415	84.31
SGT077	27308034	27308034	23450991	85.88	22904031	83.87
SGT161	27566691	27566691	23668265	85.86	23170780	84.05
SGT187	29730857	29730857	25554609	85.95	24894597	83.73
SGT230	30415770	30415770	26257368	86.33	25639411	84.30
SGT238	29472514	29472514	25386147	86.13	24773292	84.06
SGT241	29513223	29513223	25365246	85.95	24539542	83.15
SGT274	30394832	30394832	26242677	86.34	25693406	84.53

espinos/results.primary.analysis.txt · Last modified: 2017/05/24 13:50 (external edit)

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